Wadingtons have a nice weight to them so I feel I can tie flies with less added weight. I believe, maybe I'm wrong, but a waddington shank fly tied sparse with materials that still lend itself to a large profile (long spey hackle, bird fur, ostrich herl "feelers") that the fly can get down faster and be easier for me to cast. Clipped hooks around pets, kids and me have been known to get lost and then uncomfortably found later. I do tie on both and also on cotter pins for shanks. I guess I tend to put my steelhead flies on to waddingtons more and my saltwater patterns more on clipped hook shanks. I have started using junction tubing on the back of the waddingtons to hold the hook, something I've not yet figured out how to do on a skinny clipped hook shank. If I'm tying in loops of braided line for the hook it seems that I would not need the waddington and a cotter pin or clipped shank might be fine. If you want to rig that hook at the end of the shank in a manner that will allow it to pull free of the fly potentially get the fly out of the mouth of the fish then a waddington might be a better method.

Kimosabe, the cotter pins that I have seem to have a somewhat rolled edge and I've not noticed any burrs that would make me call them abrasive. I have fished them in the salt water quite a bit over the past summer, lots of 2-3 hour outings and some fish here and there that have put a pull on the line. I've never had one break off that left me with a cut loop (I've been using a small loop for a while now). If they were abrasive these loops should be coming back cut. I know your question was waddingtons versus cut hook shanks. Sorry for introducing cotter pins. I'm not recommending you go that route if you feel it will in any way compromise your fishing/catching results. I had read about them, got interested and bought a bunch. I went from cut shanks to cotter pins then to the more costly waddington shanks. I guess since I have a supply of each now I have more choices available to me. A split ring could be a good remedy, maybe even an abraision resistant loop of low diameter braided line? So far I've not felt that I've needed anything between tippet and cotter pin eye.

Do you have, or can you find an inexpensive rock tumbler/polisher? Cotter pins with a bit of grit on tumble might smooth the edges enough to make you more confident that they'll not cut your line. Everyone had a rock tumbler as a kid, right? The price of the cotter pins I got were 2000 assorted sizes for $20. I think I got 250 each of 8 different sizes.

Just to throw in a vote of confidence for cotter pins--I've caught boatloads of fall chinook and probably a quarter as many steelhead over the years on MOAL's tied with cotter pins, and I've never had problems with abrasion on the tippet or the stinger material. I assume that quality will vary, so it may pay to shop around, but considering how inexpensive they are... Another option is spinnerblade wire used in custom spinner tackle kits. It's inexpensive, available in bulk, and unlike cotter pins you can easily adjust the length.